[2024-01-24 13:27:31,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference
[2024-01-24 13:27:32,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:32,563] [INFO] Task started: Prodigal
[2024-01-24 13:27:32,563] [INFO] Running command: gunzip -c /var/lib/cwl/stga2890e80-e41d-48d4-9389-cf2b30840a1f/GCF_030295425.1_ASM3029542v1_genomic.fna.gz | prodigal -d GCF_030295425.1_ASM3029542v1_genomic.fna/cds.fna -a GCF_030295425.1_ASM3029542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:45,717] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:45,718] [INFO] Task started: HMMsearch
[2024-01-24 13:27:45,718] [INFO] Running command: hmmsearch --tblout GCF_030295425.1_ASM3029542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference/reference_markers.hmm GCF_030295425.1_ASM3029542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:46,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:46,026] [INFO] Found 6/6 markers.
[2024-01-24 13:27:46,075] [INFO] Query marker FASTA was written to GCF_030295425.1_ASM3029542v1_genomic.fna/markers.fasta
[2024-01-24 13:27:46,075] [INFO] Task started: Blastn
[2024-01-24 13:27:46,075] [INFO] Running command: blastn -query GCF_030295425.1_ASM3029542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference/reference_markers.fasta -out GCF_030295425.1_ASM3029542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:46,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:46,910] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:46,910] [INFO] Target genome list was writen to GCF_030295425.1_ASM3029542v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:46,930] [INFO] Task started: fastANI
[2024-01-24 13:27:46,931] [INFO] Running command: fastANI --query /var/lib/cwl/stga2890e80-e41d-48d4-9389-cf2b30840a1f/GCF_030295425.1_ASM3029542v1_genomic.fna.gz --refList GCF_030295425.1_ASM3029542v1_genomic.fna/target_genomes.txt --output GCF_030295425.1_ASM3029542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:03,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:03,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:03,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:03,278] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:03,278] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:03,278] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	79.4347	494	1508	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.7057	356	1508	95	below_threshold
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	75.4226	76	1508	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	75.389	119	1508	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.3595	190	1508	95	below_threshold
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	75.3546	58	1508	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	75.3103	64	1508	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	75.2514	122	1508	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.2284	142	1508	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	75.2216	58	1508	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.1514	200	1508	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	75.1113	157	1508	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	75.0694	112	1508	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	75.036	190	1508	95	below_threshold
Streptomyces hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	74.8571	225	1508	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	74.8012	220	1508	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	74.7941	78	1508	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	74.759	234	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:03,280] [INFO] DFAST Taxonomy check result was written to GCF_030295425.1_ASM3029542v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:03,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:03,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:03,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference/checkm_data
[2024-01-24 13:28:03,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:03,327] [INFO] Task started: CheckM
[2024-01-24 13:28:03,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295425.1_ASM3029542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295425.1_ASM3029542v1_genomic.fna/checkm_input GCF_030295425.1_ASM3029542v1_genomic.fna/checkm_result
[2024-01-24 13:28:53,315] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:53,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:53,335] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:53,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:53,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295425.1_ASM3029542v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:53,336] [INFO] Task started: Blastn
[2024-01-24 13:28:53,336] [INFO] Running command: blastn -query GCF_030295425.1_ASM3029542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed39228-333b-44a5-a374-0dc060edf389/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295425.1_ASM3029542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:54,533] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:54,538] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:54,538] [INFO] Target genome list was writen to GCF_030295425.1_ASM3029542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:54,600] [INFO] Task started: fastANI
[2024-01-24 13:28:54,600] [INFO] Running command: fastANI --query /var/lib/cwl/stga2890e80-e41d-48d4-9389-cf2b30840a1f/GCF_030295425.1_ASM3029542v1_genomic.fna.gz --refList GCF_030295425.1_ASM3029542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295425.1_ASM3029542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:06,423] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:06,441] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:06,441] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002297665.1	s__Holophaga sp002297665	82.4852	736	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298155.1	s__Holophaga sp002298155	82.3047	668	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165415.1	s__Holophaga sp003165415	80.0755	589	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428885.1	s__Geothrix fermentans	79.4206	491	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714685.1	s__Geothrix sp016714685	79.3658	444	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_013390615.1	s__Geothrix sp013390615	79.137	488	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334395.1	s__Geothrix sp013334395	79.1083	399	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863195.1	s__Geothrix sp903863195	78.953	463	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_002068835.1	s__Holophaga sp002068835	78.947	345	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	98.95	98.95	0.82	0.82	2	-
GCA_016721195.1	s__Geothrix sp016721195	78.9232	480	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538615.1	s__Geothrix sp003538615	78.7709	373	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192145.1	s__JAFDVN01 sp016192145	78.3995	373	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__JAFDVN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859955.1	s__Holophaga sp017859955	78.338	328	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884655.1	s__Geothrix sp903884655	78.2198	409	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.96	99.93	0.97	0.97	3	-
GCA_903876615.1	s__Geothrix sp903876615	77.8635	247	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319925.1	s__Holophaga sp002319925	77.8191	260	1508	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,443] [INFO] GTDB search result was written to GCF_030295425.1_ASM3029542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:06,444] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:06,449] [INFO] DFAST_QC result json was written to GCF_030295425.1_ASM3029542v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:06,449] [INFO] DFAST_QC completed!
[2024-01-24 13:29:06,449] [INFO] Total running time: 0h1m35s